2JPN
Solution Structure of T4 Bacteriophage Helicase Uvsw.1
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-15N HSQC | 1.66 mM [U-99% 13C; U-99% 15N] UvsW.1 | 95% H2O/5% D2O | 0.02 | 6.5 | ambient | 298 | |
2 | 2D 1H-13C HSQC | 1.66 mM [U-99% 13C; U-99% 15N] UvsW.1 | 95% H2O/5% D2O | 0.02 | 6.5 | ambient | 298 | |
3 | 3D HNCA | 1.66 mM [U-99% 13C; U-99% 15N] UvsW.1 | 95% H2O/5% D2O | 0.02 | 6.5 | ambient | 298 | |
4 | 3D HN(CO)CA | 1.66 mM [U-99% 13C; U-99% 15N] UvsW.1 | 95% H2O/5% D2O | 0.02 | 6.5 | ambient | 298 | |
5 | 3D CBCA(CO)NH | 1.66 mM [U-99% 13C; U-99% 15N] UvsW.1 | 95% H2O/5% D2O | 0.02 | 6.5 | ambient | 298 | |
6 | 3D HNCACB | 1.66 mM [U-99% 13C; U-99% 15N] UvsW.1 | 95% H2O/5% D2O | 0.02 | 6.5 | ambient | 298 | |
7 | 3D C(CO)NH | 1.66 mM [U-99% 13C; U-99% 15N] UvsW.1 | 95% H2O/5% D2O | 0.02 | 6.5 | ambient | 298 | |
8 | 3D H(CCO)NH | 1.66 mM [U-99% 13C; U-99% 15N] UvsW.1 | 95% H2O/5% D2O | 0.02 | 6.5 | ambient | 298 | |
9 | 3D HCCH-COSY | 1.66 mM [U-99% 13C; U-99% 15N] UvsW.1 | 95% H2O/5% D2O | 0.02 | 6.5 | ambient | 298 | |
10 | 3D 1H-13C NOESY | 1.66 mM [U-99% 13C; U-99% 15N] UvsW.1 | 95% H2O/5% D2O | 0.02 | 6.5 | ambient | 298 | |
11 | 3D 1H-15N NOESY | 1.66 mM [U-99% 13C; U-99% 15N] UvsW.1 | 95% H2O/5% D2O | 0.02 | 6.5 | ambient | 298 | |
12 | 3D HCCH-TOCSY | 1.66 mM [U-99% 13C; U-99% 15N] UvsW.1 | 95% H2O/5% D2O | 0.02 | 6.5 | ambient | 298 | |
13 | 2D 1H-15N HSQC, Steady state {1H}-15N NOE | 1.66 mM [U-99% 13C; U-99% 15N] UvsW.1 | 95% H2O/5% D2O | 0.02 | 6.5 | ambient | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 600 |
2 | Bruker | AVANCE | 800 |
NMR Refinement | ||
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Method | Details | Software |
torsion angle dynamics, molecular dynamics | ARIA 1.2 was used to calculate 100 structures. AMBER 9 was used to refine 20 low energy structures using GBSA solvation method. | NMRPipe |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 20 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | data analysis | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
2 | processing | Felix | 2000 | Accelrys Software Inc. |
3 | peak picking | Felix | 2000 | Accelrys Software Inc. |
4 | chemical shift assignment | Felix | 2000 | Accelrys Software Inc. |
5 | chemical shift assignment | ARIA | 1.2 | Linge, O'Donoghue and Nilges |
6 | structure solution | ARIA | 1.2 | Linge, O'Donoghue and Nilges |
7 | refinement | Amber | 9 | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Koll |
8 | data analysis | ProcheckNMR | Laskowski and MacArthur | |
9 | restraint generation | TALOS | Cornilescu, Delaglio and Bax |